sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
dcc0d0c1fc9439b7120b7cc3afbd9ca70957331a24c7024a59d658626a8a8d77 | Java | 6,838 | 268 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0e693defbbf8a1937cc75e1ec0cfd3c703b5fdce815d3415a8627ec58fdb854e | Java | 6,842 | 199 | /*
* Copyright (C) 2015 adriaan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distribute... |
d193f724b1b9ba2b2063b2cd79bc5e94d355087d7841ef17654c07c9424d6f35 | Java | 6,848 | 159 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map.Entry;
imp... |
d0a6765cb6c1a6835e7495edbf940d3387c50cca9ece505c37345b54f2cc368d | Java | 6,851 | 232 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica.io.... |
55b49599bb6c5e95e556176b5e3c64814fbbb9f8fa888199f58110dae250950b | Java | 6,860 | 239 | package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import cern.jet.stat.tdouble.Probability;
import java.math.BigDecimal;
import java.math.MathContext;
import java.math.RoundingMode;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
*
* @author Patrick De... |
c4e4bda013d4cf4486518747cf06f2d0bb73254ee3ad4c1a44b9155746c2a7ae | Java | 6,864 | 212 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import umcg.genetica.io.hpo.HpoOntology;
import com.opencsv.CSVParser;
import com.o... |
15096764a008004ceb94bb5e17fd6a4ecd3b80ad54b11b164999d00362d89b1e | Java | 6,867 | 206 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
43d03b93cecc30f36ab12369167bd249765d76e6c98e8d1d6cfc2b97d627face | Java | 6,868 | 182 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
4970e33b439d806a3058b7fdb631a26d12e12bfaf40320ce24b4489c85ad1af2 | Java | 6,869 | 214 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.textmeta;
import eqtlmappingpipeline.util.QTLFileSorter;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.... |
173b444a9f7b1aee559694f64204e0de391f9f24b9c1dd38c394284dfdbcfcc7 | Java | 6,885 | 141 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetics.tableAdaption;
import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import ja... |
f127bafc7b5ef52d25e5ce1b17311b6d73109d569b9dd778b1fd2cdc5a918b40 | Java | 6,898 | 287 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
import umcg.genetica.console.ConsoleGUIElems;
import umcg.genetica.console.ProgressBar;
import java.io.IOException;
import java.util.HashMap;
import java.util.zip.DataFormatExcep... |
b4d79d5945a27eac7ec21678ed674beff5ed515669e0770816fe44c1e190412a | Java | 6,909 | 192 | /*
* Copyright (C) 2015 adriaan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distribute... |
a36d11d1189c118148f3572b408ae3f17f3e1d7e146a5f2c0b9c0188c1c62c63 | Java | 6,935 | 238 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import umcg.genetica.io.trityper.probeannotation.ProbeTranslation;
import eqtlmappingpipeline.binarymeta.meta.graphics.ZScorePlot;
import java.util.ArrayList;
import java.uti... |
5dad1601b79ae4cd7200886f88c1ba194dd46352eef7397e7a0482f01df624ca | Java | 6,944 | 158 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
8f6035b859c25391348fa4dbd7c9b77abf5e51b559b87c46ce8d5f0beaf0c45c | Java | 6,946 | 180 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
1a9ea17173b777cf127a2ddd0ded5b173c3927289eee4592addf56ebcb61c04e | Java | 6,948 | 224 | package umcg.genetica.math.matrix2;
import org.apache.commons.io.input.CountingInputStream;
import org.apache.commons.io.output.CountingOutputStream;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.text.TextFile;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.channels.Channels;
import... |
5615e03ea48a05375891dce14be76fa38f32c0153e59270d4c2eb2ef2d639ad9 | Java | 6,948 | 189 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVParser;
import co... |
6d48995329c3d141e35621571b7c4deb031fe2251172cd35326f064a94e0642d | Java | 6,965 | 275 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import org.jdom.IllegalDataException;
/**
*
* @author adriaan
... |
3cee8c7e401c27f3fe4d9247a42c062cd343ed7adc1cfb6f5b482be45fac7a2d | Java | 6,998 | 183 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
85bc856e753fc3dbde375db9990564f5c59386c5b8e1c1e8b759bb87f0404bf6 | Java | 7,040 | 245 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.bin;
import com.mastfrog.util.streams.HashingOutputStream;
import java.io.*;
import java.security.NoSuchAlgorithmException;
import java.util.zip.GZIPInputStream;
import java.util.zip... |
d17f434ac1a25ae739ce81465ddfcc80432800f90edb601ab9f2e0e5f3524703 | Java | 7,043 | 196 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.toolbox;
import nl.systemsgenetics.toolbox.picalo.OverlapPicEqtlWithGwas;
import java.io.File;
import java.... |
2dc237ccabdf4b7a40fa61bce3a8e14dc34a78c8706246fa74f06d26c3f10213 | Java | 7,066 | 198 | package umcg.genetica.io.trityper.converters;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.BaseAnnot;
import umcg.genetica.text.Strings;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
publi... |
95b119699370d628af1a34030e22f8e390f8f2795a4f1ce3005b27294342ebf3 | Java | 7,075 | 202 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
38a9c40d80ef7e2aa710d57a1fea539d4c5e7fea309bbae3fe930eeb3dfeb9cd | Java | 7,087 | 189 | /*
* DetermineLD.java
*
* Created on August 8, 2006, 4:32 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package mbqtl.vcf;
import umcg.genetica.containers.Pair;
/**
* @author Lude Franke
*/
public class DetermineLDVCF {
public final static int IN... |
b3f734939d28470a5cf9c957fe2396b97e43d4c2899d86209c30238bf6f8d5ab | Java | 7,100 | 176 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
a9b59fd0df1f2bf468ebea29ec1c9c27a6949577618b05fea6fc18077316b2b8 | Java | 7,112 | 215 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
ab1a0edea278fd4e8c8bf3a825dcb70ae1050c9babcfaca6a345a878a4f7ba69 | Java | 7,117 | 168 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
782018d0468cbd244d704706a0e77b684fba498605d3dfcf052b43ecd43a9662 | Java | 7,124 | 183 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import umcg.genetica.io.hpo.HpoOntology;
import com.opencsv.CSVParser;
import com.o... |
e5a0f60f12ac0d8c37f19e19762b78876d9b7159dbc42ff30600b22c9f1a4117 | Java | 7,129 | 184 | package eqtlmappingpipeline.binarymeta.meta;
import eqtlmappingpipeline.binarymeta.meta.graphics.ZScorePlot;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.zip.DataFormatException;
import umcg.... |
12a887a8c43b4be87a67952f20535e8f36c197783343133a870311c4a8db1376 | Java | 7,138 | 175 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may... |
bd444b5a80cf1f4f5d4aac25b4d6662abb596317bfceab7b18a8c14a20992ca5 | Java | 7,174 | 230 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
d1312d662284e12fe02dde5912b0288223b2de3f65e762c68f5f0d37dbacfc7d | Java | 7,190 | 190 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
f7998c1494fed25f9f25e3148998a725af18530145f43b8dcf886360cdc05980 | Java | 7,192 | 160 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.graphics;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.File;
import umcg.genetica.math.stats... |
2602b45ead779db2380de0f892f4e63ddb949bb78f261e3b3555ddc03faeb785 | Java | 7,240 | 177 | package mbqtl.datastructures;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import umcg.genetica.features.Gene;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashS... |
4a46abfe83905bd1da430991834e27069b768c9cbfb0c680f9280370764c8248 | Java | 7,258 | 175 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlannotation;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.ut... |
5ced47b4825e6209a41cd2ee710f62140f5a01fc67c385a8457a88ab0351bb5f | Java | 7,258 | 221 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.probeannotation;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import java.io.IOException;
import java.util.HashMap;
/**
*
* @author ha... |
a9772ee4e16dc8c8fdd57de6e85c3972fe15411c2f800c91f56fcdc3d5e61639 | Java | 7,262 | 247 | package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import cern.jet.stat.tdouble.Probability;
import java.math.BigDecimal;
import java.math.MathContext;
import java.math.RoundingMode;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
*
* @author Patrick De... |
4d64bd63d501c74624719d7a071bb4d4c82009da3ab684acc3647c3ddfe669bb | Java | 7,277 | 152 | package ebi.spot.neo4j2owl;
import ebi.spot.neo4j2owl.importer.N2OCSVWriter;
import ebi.spot.neo4j2owl.importer.N2OImportResult;
import ebi.spot.neo4j2owl.importer.N2OImportService;
import org.junit.Test;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Result;
import org.neo4j.kernel.impl.proc.... |
c2744d310d786e10a7882ae1b30533a4e1eb63fd208b62b7106595ca906fd101 | Java | 7,292 | 330 | package org.molgenis.genotype;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
public final class Alleles implements Iterable<Allele>, Comparable<Alleles... |
f8f2b4383c5a560b08e0382503390ba353eb99388dbce0af8b74d915f3334c64 | Java | 7,302 | 178 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.text.converters;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;... |
f5fcc77f6ec1368473c627e25399b878df1155258c1284fe32b79163a67d3346 | Java | 7,318 | 222 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import eqtlmappingpipeline.binarymeta.meta.MetaSettings;
import java.io.IOException;
im... |
264c529f5abf90ef08d2dc570609588d370b4cd1e2f03de076f5abec22408228 | Java | 7,345 | 209 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
6ab9635d212b3c237d1d4ac86196409b7ed7a59d79c86e226021cde902dc52ac | Java | 7,346 | 192 | /*
* This class was freely translated from R BioConductor package "qvalue"
* Storey JD. (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B, 64: 479-498.
* Storey JD and Tibshirani R. (2003) Statistical significance for genome-wide studies. Proceedings of the Nationa... |
0f6e5274e0beac17f0d81d47f6c51481494e56746f30d58212cd6051ee92f59d | Java | 7,360 | 191 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
993856df53c7f6c854961e68d68e7fdf449a75cc3c7f6a01b196d9ea406c6ff0 | Java | 7,363 | 213 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
82b2bba33827d475f8acf75511a757bae8f99bcf26c554602b7186240c1e59f2 | Java | 7,365 | 241 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.Allel... |
5ce4ace13c7821f55ce0353794b63173997300a44042c4ae32ce4ca0fdfc53f5 | Java | 7,370 | 168 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
8a7761361c4aef1755f9b28da2f106606e552c128a93215d67dbdca9e2cb9a51 | Java | 7,389 | 229 | package org.molgenis.genotype.variant.range;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.... |
42b979510e870691c2e93c9bd66a8c4a74a4065535b6aedbc8d545234dc4a648 | Java | 7,408 | 197 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.BufferedOutputStream;
import java.io.DataOutputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import umcg.genetica.io.Gpio;
import umcg.... |
d5498d4382f035cecd70e5cdf4eb66f132116766f7636f8bcbbd40f8fab65799 | Java | 7,446 | 187 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
2477d45fa856810bc8078e2f6eed6777e4ecaf582870b94cf66ea6cc009604a2 | Java | 7,467 | 154 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetics.tableAdaption;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashS... |
7154740d4344969271af73f8330093a59827887df0b7595538c904de098b9b31 | Java | 7,471 | 283 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.genomicboundaries;
import java.util.Iterator;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class GenomicBoundariesTest {
p... |
ffc5f0262483d67d1b0a85266263614a922fb6dc396d3553cc07087df4076900 | Java | 7,483 | 211 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
0689f34a66941c929ddcd2e1670a24136f5d5d5e096b246144a0826481b2e8dd | Java | 7,531 | 147 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
32e36c16a9d41cd76514a508903a74a69e0c8443bffc756586bf346f1d2ed355 | Java | 7,534 | 209 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
da969c0f78a9d8caecf99d20031507ef860c7ba82ced9b679e03db4a04b3b0ae | Java | 7,592 | 239 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
7a2fb7040ea6e3da7e470821c2294c60bffe81a6d91e2dacec40008fb1e1250b | Java | 7,631 | 227 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.C... |
d6bfdb5597c94919ec470aa58e6cb5f872270541031aa3c77c4bdbc4150bfb20 | Java | 7,640 | 182 | package umcg.genetica.io.binInteraction;
import java.util.Arrays;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionZscores {
private final int[] samplesInteractionCohort;
private final double[] zscoreSnpCohort;
private final double[] zscoreCovariateCohort;
private final double[] zscoreInteracti... |
20f3f16e7dd1ccb1489ec0713fb25b2d4b9c5229d0b0fa1231dd62eda13021ad | Java | 7,642 | 301 | package edu.cmu.cs.eyetrack.state;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
import edu.cmu.cs.eyetrack.helper.Coordinate;
i... |
6a17a8da6fbdb52e02cbff42e989e1c00300be56b674d216e175723585e67c8e | Java | 7,659 | 227 | /*-
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must ret... |
4de4a1b7d8050aa374eebe2ba3399d9a66190c1e28d9b809e01d794256f9c1ab | Java | 7,703 | 219 | package org.molgenis.genotype.trityper;
import java.io.*;
import java.util.HashSet;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.Gen... |
dc3d0c7a26bcbd3ae17fcccc9c2e5598163b4c768c29dd1e630a18405abab85e | Java | 7,708 | 221 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashMap;
import java.uti... |
10251c7474a6e9057e4c54790dba34d3fc923209452f60cd13023b2caf017940 | Java | 7,717 | 174 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
c40a73af067738ae4110d4b5375732c605d4e90ac4486cf176b48252ba2b98c1 | Java | 7,726 | 202 | package umcg.genetica.math.matrix2;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.File;
import java.io.IOException;
import java.util.stream.IntStream;
public class DoubleMatrixDatasetRandomAccessTranspo... |
ea88afd8ff55f5c9354f5695dae9d8f78ab1b6802676dbfd26546c2015c5a535 | Java | 7,729 | 237 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
a98ecbe6796c48c0373ed001e50489a1faf02550c08884c1009a22fb204e0f2d | Java | 7,742 | 194 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
i... |
9890617892b64d1546883d20871c20f1d6b9755d09a1786173af3890ff794a19 | Java | 7,753 | 256 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.features.Feature;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import java.awt.*;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.HashSet;
/**
* Creat... |
282a83ccb8d35a1a0a135fa7283199ed97393cc48737d15b6b265408191207cc | Java | 7,819 | 246 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
8c5b9cc50757e8a5d4aeb9b198f6338469bea599431d55f60e49209766ef1cea | Java | 7,823 | 217 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
faacc7977aa9a30485848ed33525ae5cdaf8aed8ae8df9159041d54c519ad0fb | Java | 7,894 | 260 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
4b3ee10d74b806d93180deea5c72ba83689d2c2575967df5ff08190a9c8770f3 | Java | 7,909 | 206 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
17e6dacfe2b862c511c0c17181e0de3a5fb9c9ea144e08064de425bbb8196a24 | Java | 7,918 | 229 | package mbqtl.vcf;
import org.broad.tribble.readers.TabixReader;
import umcg.genetica.features.Feature;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
... |
da6ca5c15414d6b32ee91ad6fed76002cad896e0543bf4420bade328e0185d26 | Java | 7,948 | 181 | ///*
// * DetermineLD.java
// *
// * Created on August 8, 2006, 4:32 PM
// *
// * To change this template, choose Tools | Template Manager
// * and open the template in the editor.
// */
//
//package imputationtool.preprocessing;
//
//import java.lang.Math;
//import metaqtl2.Containers.GenDataset;
//import metaqtl2.Con... |
181e94d49678dca7caa09df0ab23ec287eddd84a08768d92eb1e830beefd1b0b | Java | 7,959 | 246 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
5a15c9b6090a1ec3f0d26f5e777902a977d32676af4af2a3d2786e2219137058 | Java | 7,960 | 236 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
ee05a9e9cd5e7791d2d0218def9669147c8d57dfe2adc133f789f34e029d75e6 | Java | 7,990 | 216 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
ac934f19b82eb5965f00acbfb3e3176d62fde61e5b4afdd31cce31fa0e151c8a | Java | 7,993 | 219 | package edu.cmu.cs.eyetrack.test;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Map;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import au.com.bytecode.opencsv.CSVWriter;
import edu.cmu.cs.eyetra... |
dadb33bd266c430c0755471f7c327477656893a5a591eb147532d652192686dc | Java | 8,052 | 230 | package umcg.genetica.math.stats;
import org.apache.commons.math3.linear.SingularMatrixException;
import org.apache.commons.math3.stat.regression.OLSMultipleLinearRegression;
import umcg.genetica.containers.Pair;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.util.*;
import java.util.concurrent.at... |
0ece452a7a6c0fd55fa5c301628969bede27c3876302c925b1cc28901d0d7ee0 | Java | 8,059 | 240 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
cf7ca1ba91e9b9f830b0765326568525574cb6a8ed573b50c11f128ac8fa0602 | Java | 8,068 | 245 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.development;
import cern.jet.math.tdouble.DoubleFunctions;
import com.opencsv.CSVParser;
impor... |
e690e1942ed43ccfeab691ec819192305c5a13e356fcf4c4490420910fe1cf04 | Java | 8,109 | 273 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
040b59f2f3c92d3fa0756ddb4450ce8d0eae7b63bb79d5f19e988faa4239cb2c | Java | 8,133 | 213 | /*
* This program checks for batch effects within beagle imputed dataset batches
*/
package imputationtool.postprocessing;
import java.io.File;
import java.io.IOException;
import java.util.regex.Pattern;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.stats.WilcoxonMannWhitney;
/**
*
* @author ha... |
ffe1f01f4dd7026aea293dee9ec26ab5881c547e683fafa74dd3eb7e053dd8b1 | Java | 8,169 | 180 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.geofiles;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
import java.io.... |
c640f7f00356bda5507186722081788d888f17d0935b975985c679d616e3a736 | Java | 8,172 | 188 | package mbqtl;
import mbqtl.vcf.DetermineLDVCF;
import mbqtl.vcf.VCFTabix;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.containers.Pair;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.Feature;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.tex... |
f69e5137f8214c838350f9d225fa7da0181b820dd64c0bbc42de63fb90af92b5 | Java | 8,196 | 305 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import java.awt.*;
import java.text.DecimalFormat;
/**
* Created by hwestra on 9/12/15.
*/
public class HeatmapPanel extends Panel {
private double[][] data;
private Range range;
private S... |
a5e9bddbdc76907c0f84644727e2c961d132190e92a1048e18dfb40450eb114c | Java | 8,206 | 183 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
d4003c7815378e5a08a49d0d489968faca65e8ab3111bd4caa3df993691d46ec | Java | 8,207 | 234 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.nio.Buffer;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
/**
* @author harm-jan
*/
pu... |
8da36cd8240be95a90556b1034c8e8ee8d7a4a43da3a959f7dd3e348ff15a9ec | Java | 8,213 | 234 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.editable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
imp... |
7052aa21565fcd5f3f71349914b701f0f5df3507e56027249101829a1bfa3426 | Java | 8,222 | 199 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
e99030b503f4bc739ae8a76b64b76d0bf0bf8053e828e3baa9e1b3d66072e284 | Java | 8,230 | 171 | package org.molgenis.genotype.multipart;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.ResourceTest;
import org.molgenis.genotype.annotation.Annotation;
import org.molgenis.genotype.annotation.SampleAnnotation;
import org.molgenis.genotype.annotation.VcfAnnotation;
import org.molg... |
3e0f76cdc7835335d2fe8bec696ee7a6ac79608f88ed512fb4a4887422b64138 | Java | 8,260 | 231 | package edu.cmu.cs.eyetrack.test;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import au.com.bytecode.opencsv.CSVWriter;
import edu.cmu.cs.eyetrack.analysis.io.Loader;
import edu.cmu.cs.eyetrack.analysis.score.PointB... |
dadffdfd8bcc04cf2335ca5b2fc27f8185793df72f3367c2198f625c297d53d1 | Java | 8,327 | 225 | package edu.cmu.cs.eyetrack.analysis.score;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import edu.cmu.cs.eyetrack.analysis.score.compare.PointComparator;
import edu.cmu.cs.eyetrack.analysis.score.distance.DistanceFunction;
import edu.cmu.cs.eyetrack.analysis.struct.Trajectory;
import edu.c... |
e3f603f23ca30fbc2dea559f1ea18ea2ed9376a2d01260a32913fd4a8486e7c9 | Java | 8,339 | 262 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatr... |
c4e69d4d28f915602558b430bede2bb4904a879082851a5eae2bd9abf045ad76 | Java | 8,341 | 353 |
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.QTLTextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import umcg.genetica.text.Strings;
import ja... |
75914d052d226270024c81ec7335a597b454af15c201845c5be66c9d6893dda6 | Java | 8,390 | 261 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
eed26d8e508d535156f3be8365b8990e21d2c898c2d1e167650cf90fcc031258 | Java | 8,415 | 261 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import org.m... |
b0f105d6d09b877b7a75cd3d8fc3da68b9eebf4d814ba5439dcce003f6454cf8 | Java | 8,428 | 257 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.bondermj.pcoa;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.ap... |
b01c5d2ae0ddc116469fe1c0a999d90e115d7814ae62a20db01fcc5046af2c62 | Java | 8,435 | 265 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
209da1c0a1f3df70046f1e458db656282348dc3f32fc16a2c2d2cb2e5a72d819 | Java | 8,442 | 236 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
e9ab0214352024b9782aec21d521748fff0e770bbe32a6e36b119fde230d6ef7 | Java | 8,447 | 256 | /*-
* #%L
* Utility methods for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the ... |
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